#!/usr/local/bin/perl

###############################################################################
# Program     : defaultBuildsPepsProts
# Author      : Terry Farrah 
# $Id: main.cgi 5994 2009-03-06 08:01:38Z dcampbel $
#
# Description : This script displays details about all Atlas builds
#
# SBEAMS is Copyright (C) 2000-2021 Institute for Systems Biology
# This program is governed by the terms of the GNU General Public License (GPL)
# version 2 as published by the Free Software Foundation.  It is provided
# WITHOUT ANY WARRANTY.  See the full description of GPL terms in the
# LICENSE file distributed with this software.
#
###############################################################################


###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
use vars qw ($q $sbeams $sbeamsMOD $PROG_NAME
             $current_contact_id $current_username);
use lib qw (../../lib/perl);
use CGI::Carp qw(fatalsToBrowser croak);

use SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::DataTable;
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Connection::TabMenu;

use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::PeptideAtlas;
$sbeamsMOD->setSBEAMS($sbeams);


###############################################################################
# Global Variables
###############################################################################
$PROG_NAME = 'defaultBuildsPepsProts';
main();


###############################################################################
# Main Program:
#
# Call $sbeams->Authentication and stop immediately if authentication
# fails else continue.
###############################################################################
sub main
{
    #### Do the SBEAMS authentication and exit if a username is not returned
    exit unless ($current_username = $sbeams->Authenticate(
        permitted_work_groups_ref=>['PeptideAtlas_user','PeptideAtlas_admin',
        'PeptideAtlas_readonly', 'PeptideAtlas_exec'],
        #connect_read_only=>1,
        allow_anonymous_access=>1,
    ));


    #### Read in the default input parameters
    my %parameters;
    my $n_params_found = $sbeams->parse_input_parameters(
        q=>$q,
        parameters_ref=>\%parameters
        );

    if ( $parameters{reset_id} && $parameters{reset_id} eq 'true' ) {
      $sbeamsMOD->clearBuildSettings();
    }

    ## get project_id to send to HTMLPrinter display
    my $project_id = $sbeamsMOD->getProjectID(
        atlas_build_name => $parameters{atlas_build_name},
        atlas_build_id => $parameters{atlas_build_id}
        );


    #### Process generic "state" parameters before we start
    $sbeams->processStandardParameters(parameters_ref=>\%parameters);


    #### Decide what action to take based on information so far
    if ($parameters{action} eq "???") {
        # Some action
 
    } else {
        $sbeamsMOD->display_page_header(project_id => $project_id);
        handle_request(ref_parameters=>\%parameters);
        $sbeamsMOD->display_page_footer();
    }

} # end main


###############################################################################
# Show the main welcome page
###############################################################################
sub handle_request {
  my %args = @_;

  #### Process the arguments list
  my $ref_parameters = $args{'ref_parameters'}
  || die "ref_parameters not passed";

  my %parameters = %{$ref_parameters};


  #### Get the current atlas_build_id based on parameters or session
  my $atlas_build_id = $sbeamsMOD->getCurrentAtlasBuildID(
    parameters_ref => \%parameters,
  );
  if (defined($atlas_build_id) && $atlas_build_id < 0) {
    #### Don't return. Let the user pick from a valid one.
    #return;
  }


  #### Get the HTML to display the tabs
  my $tabMenu = $sbeamsMOD->getTabMenu(
    parameters_ref => \%parameters,
    program_name => $PROG_NAME,
  );
  if ($sbeams->output_mode() eq 'html') {
    print $tabMenu->asHTML();
    print "<BR>\n";
  }


    #### Read in the standard form values
    my $apply_action  = $parameters{'action'} || $parameters{'apply_action'};
    my $TABLE_NAME = $parameters{'QUERY_NAME'};


    #### Set some specific settings for this program
    my $PROGRAM_FILE_NAME = $PROG_NAME;
    my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";
    my $help_url = "$CGI_BASE_DIR/help_popup.cgi";


    #### If the output_mode is HTML, then display the form
    if ($sbeams->output_mode() eq 'html') {

        print qq~
        <script LANGUAGE="Javascript">
          function switchAtlasBuild() {
            document.AtlasBuildList.apply_action.value = "GO";
            document.AtlasBuildList.submit();
          }
         document.title = 'PeptideAtlas: Download Builds Peps & Prots';
        </script>
        ~;

        print $q->start_form(-method=>"POST",
                             -action=>"$base_url",
			     -name=>"AtlasBuildList",
                            );
  print qq~
  <div style='margin-left:15px;margin-top:25px;min-height:600px;'>
     Links below will retrieve the identified peptides and proteins
     for the latest PeptideAtlas build for each organism.<br>
     These URLs stay constant over time and can be used programmatically.
     <br><br>
  ~;


  my $table = SBEAMS::Connection::DataTable->new(CELLPADDING=>5);

  my $this_row = $table->getRowNum();

  my $org_idx = 0;
  my $distinct_peps_idx = 1;
  my $n_canonicals_idx = 2;
  my $ncols = 3;

  my @headers;
  $headers[$distinct_peps_idx] = 'distinct peptides';
  $headers[$org_idx] = 'Organism';
  $headers[$n_canonicals_idx] = 'canonical proteins';

  # Define header row
  $table->addRow( \@headers );
  $table->setRowAttr(  COLS => [1..$ncols], ROWS => [1], BGCOLOR => '#002664', ALIGN=>'CENTER' );
  $table->setHeaderAttr( WHITE_TEXT => 1, BOLD => 1 );

  my @organisms = ('Human', 'Mouse', 'Pig', 'Drosophila', 'C elegans', 'Yeast');

  foreach my $organism ( @organisms ) {
    my @row;
    my @trinfo;
    my $selected = '';
    my $bgcolor = '#f3f1e4';

    $row[$org_idx] = $organism;
    $row[$distinct_peps_idx] =<<"    END";
<A HREF="GetPeptides?organism_name=$organism&apply_action=QUERY&output_mode=html" TITLE="Display distinct peptides for $organism default build in browser">browser</A>,
<A HREF="GetPeptides?organism_name=$organism&apply_action=QUERY&output_mode=excel" TITLE="Retrieve distinct peptides for $organism default build in Excel format">Excel</A>,
<A HREF="GetPeptides?organism_name=$organism&apply_action=QUERY&output_mode=xml" TITLE="Retrieve distinct peptides for $organism default build in XML format">XML</A>,
<A HREF="GetPeptides?organism_name=$organism&apply_action=QUERY&output_mode=tsv" TITLE="Retrieve distinct peptides for $organism default build in TSV format">TSV</A>,
<A HREF="GetPeptides?organism_name=$organism&apply_action=QUERY&output_mode=csv" TITLE="Retrieve distinct peptides for $organism default build in CSV format">CSV</A>
    END
    $row[$n_canonicals_idx] =<<"    END";
<A HREF="GetProteins?organism_name=$organism&presence_level_constraint=1&redundancy_constraint=4&apply_action=QUERY&output_mode=html" TITLE="Display canonical protein list for $organism default build in browser">browser</A>,
<A HREF="GetProteins?organism_name=$organism&presence_level_constraint=1&redundancy_constraint=4&apply_action=QUERY&output_mode=excel" TITLE="Retrieve canonical protein list for $organism default build in Excel format">Excel</A>,
<A HREF="GetProteins?organism_name=$organism&presence_level_constraint=1&redundancy_constraint=4&apply_action=QUERY&output_mode=xml" TITLE="Retrieve canonical protein list for $organism default build in XML format">XML</A>,
<A HREF="GetProteins?organism_name=$organism&presence_level_constraint=1&redundancy_constraint=4&apply_action=QUERY&output_mode=tsv" TITLE="Retrieve canonical protein list for $organism default build in TSV format">TSV</A>,
<A HREF="GetProteins?organism_name=$organism&presence_level_constraint=1&redundancy_constraint=4&apply_action=QUERY&output_mode=csv" TITLE="Retrieve canonical protein list for $organism default build in CSV format">CSV</A>
    END

    $table->addRow( \@row );
    my $this_row = $table->getRowNum();
    $table->setRowAttr(  COLS => [1..$ncols], ROWS => [$this_row], BGCOLOR => $bgcolor, @trinfo );
  }

  my $nrows = $this_row;
  $table->setColAttr(  COLS => [$org_idx+1], ROWS => [2..$nrows], NOWRAP => 1 );
  $table->setColAttr(  COLS => [$org_idx+1], ROWS => [1..$nrows], ALIGN => 'LEFT' );
  $table->setColAttr(  COLS => [$org_idx+2..$ncols], ROWS => [1..$nrows], ALIGN => 'CENTER' );
  print "$table\n</div>\n";
  print $q->hidden( "apply_action", '');
  print $q->end_form;

  }
} # end showMainPage